Stranded protocols & study of biotypes

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Hello,

I currently use the "TruSeq Stranded Total RNA Sample Prep Kits" of Illumina. I would like to demonstrate the usefulness of this protocol compared to the "standard protocol". So, I wanted first of all to study the percentage of biotype in each protocol with the Biomart data mining tool, to see if there were big differences between the protocols. But this tool is not specific enough for me. I then wanted to study the percentage of lncRNA in each protocol, using the lncRNAdb database, and the results are rather interesting. I wanted to know if people used other tools to determine the % of non-coding RNAs, for example, in their RNA-seq experiments ?

Thanks in advance!